Isolated_left_hand_holding_smartphone-optogenetic app

Tools for Brains

Optogenetics Pro

Optogenetics is a tool which aids an investigator in calculating the required optical power for a given in-vivo experiment involving optogenetics or any other experimental approach that includes light delivery to deep brain areas via optical fibers. Different brain areas have different optical properties, which determine how light scatters and distributes, once it exits the optical fiber. To estimate the amount of light required for a given experimental design, knowledge about the specific scattering properties of the brain region of choice, the specific opsin to be used, and the properties of the optical fiber are required. Once a user inputs these parameters into the APP, it calculates the maximal depth at which excitation of the opsin can be expected. The penetration depth is plotted as a function of optical power (mW), such that a user can see how light scatters in the brain tissue under the specific circumstances.

Optogenetics includes 5 commonly used atlas pages and requires about 74MB of space to install. The Pro version has a full mouse brain atlas with 43 pages but requires 430MB to install (yes, these atlas images are VERY high resolution). All computations, interfaces etc. are the same between these two versions.

Precise Light Power Calculation:

Precise Light Power Calculation:

Provides accurate estimations of the required optical power for effective opsin activation, ensuring optimal light delivery for in-vivo optogenetic experiments.

Customized to Brain Region and Opsin:

Customized to Brain Region and Opsin:

Tailors calculations to the specific optical properties of targeted brain areas and the chosen opsin, offering highly personalized and effective experimental setups.

Visual Representation of Light Penetration:

Visual Representation of Light Penetration:

Graphically displays how light scatters and penetrates within brain tissue, aiding in understanding and planning for the depth and intensity of light exposure.

Optogenetics closeup green
Optogenetics closeup green and pink
background wire texture transparent blue

Get mroe from the App with PRO

Go PRO and access the Brain Atlas


Version 2 supports 17 different opsins and a complete light scattering brain atlas for the adult mouse that allows a user to look up the brain area of his/her choice, and read the specific scattering coefficient for this particular area.


A Pro and a Lite version are available. The two versions are identical with the exception that the Pro version includes a complete brain atlas consisting of 43 images / plates, while the atlas Lite version only has 5 plates.

How Can These APPs Help Your Research?

Optogenetics is a technology allowing users to control neural activity with light. Neurons, are naturally not light-sensitive. But we can make them light sensitive by introducing foreign light-sensitive proteins i into the brain tissue through viral vectors or genetic manipulations. These proteins respond to specific light wavelengths, such as blue, orange, or red light. Once illuminated with sufficient light at the correct wavelength, the proteins create either a depolarizing current to excite neurons or a hyperpolarizing current to inhibit them. Depending on the protein and light used, optogenetic manipulations can either increase or decrease neuronal firing. In some cases, where two proteins and two different light colors are introduced, it’s possible to achieve both effects in the same cell.

Illuminating brain tissue with light is straightforward with ex-vivo tissue sections. For in-vivo manipulations, where the brain is enclosed by bone, skin, and hair, light can be delivered into the brain tissue through inserted optical fibers connected to a light source like a laser. But determining the required laser power and understanding how light spreads in the tissue post-exit from the glass fiber are challenges. These are further complicated by the brain tissue’s diverse light scattering properties. For example, light spreads differently in the cerebellum compared to the brain stem, leading to vastly different experimental lighting requirements.

To determine the correct light requirements for a specific experimental setup, one must understand the scattering properties of the chosen brain region, the specific opsin used, and the properties of the optical fiber. Users input these parameters into the Optogenetics or Optogenetics Pro APP, which then calculates the light scattering for the specific situation. The APP includes either a simplified brain atlas with common sections/images (Optogenetics) or a full adult mouse brain atlas (Optogenetics Pro), where users can locate and mark their targeted brain area.

Technical Details:

The accuracy of the APP’s calculations was initially verified through empirical measurements. Optical fibers were moved through live mouse brain tissue blocks, and light scattering was measured as a function of distance in various brain areas with differing scattering coefficients. An entire mouse brain was also imaged under blue light (470 nm) within a carefully calibrated gray scale. The results from these two methods were then compared and calibrated, ensuring the mathematical framework’s accuracy. While empirical measurements were taken from seven brain areas, light scattering coefficients for other areas were extrapolated based on these data points, fitting well within the established calibration curve. This indicates the mathematical framework behind the approach is accurate.

Learn More About Optogenetics with PopNeuron's Mini-Series:

Documentation and Software

Niche Tools for Niche Science

Even More Tools for Brains!

Check out the latest "Tools for Brains" and additional accessories in the PopNeuron Store

"Tools Specifically Tailored for Neuroscience"